[gmx-users] crystals of KCl during simulation
baaden at smplinux.de
Mon Jun 1 14:34:55 CEST 2009
regafan at hotmail.com said:
>> [..] but after equilibration I have observed that KCl is aggregating, like
>> if it was making crystals. When I used NaCl instead KCl, this not
>> Does anybody has any idea about the reason of the behaviour of KCl in
>> the simulation?
This even does happen with Amber :) So my guess is you correctly transferred
the parameters, but stumbled upon an artefact. If you check the recent
literature you may notice that many publications with Amber using K+
only employ minimal (neutralising) salt conditions as a workaround. At
least this is what we did recently .
 Interactions between neuronal fusion proteins explored by molecular
dynamics, Biophys.J.94, 2008, 3436-3446.
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
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